aurthurm

import pandas as pd

breakpoints = pd.read_csv('Breakpoints.txt', sep='\t', low_memory=False)
antibiotics = pd.read_csv('Antibiotics.txt', sep='\t', low_memory=False)
organisms = pd.read_csv('Organisms.txt', sep='\t', low_memory=False)

# limit breakpoints to 2024 CLSI for Humans only
breakpoints = breakpoints[
    breakpoints['TEST_METHOD'].isin(['MIC', 'DISK']) & 
    (breakpoints['GUIDELINES'] == 'CLSI') & 

aurthurm

from bika.lims import api
from nmrl.lims.scripts import setup_script_environment
from senaite.core.catalog import SETUP_CATALOG, SAMPLE_CATALOG
import transaction


def fix_services():
    services = api.search({"portal_type": "AnalysisService"}, SETUP_CATALOG)
    print("Total services found: {}".format(len(services)))

aurthurm

from nmrl.lims.scripts import setup_script_environment
from bika.lims import api
import transaction
from senaite.core.catalog import SETUP_CATALOG
import re

def create_category(parent, title):
    category = api.create(parent, "AnalysisCategory", title=title)
    category.reindexObject()
    return category

aurthurm

from typing import Any, Mapping, Generic, TypeVar
from pydantic import BaseModel
from sqlalchemy import Column, String, select
from sqlalchemy.ext.asyncio import AsyncAttrs
from sqlalchemy.orm import DeclarativeBase
from sqlalchemy_mixins import ReprMixin, SerializeMixin, SmartQueryMixin, SessionMixin
from sqlalchemy_mixins.utils import classproperty
from custom_flake_uid import get_flake_uid

aurthurm

#!/usr/bin/env python
# -*- coding: utf-8 -*-

import multiprocessing
import re
import threading
import time

LAST_TIMESTAMP = -1
SEQUENCE = 0

aurthurm

"""
The SQLAlchemy Shell.

This is just a wrapper for code.InteractiveConsole with some useful
defaults for using SQLAlchemy
"""

import os
import sys
from code import InteractiveConsole

aurthurm

from sqlalchemy import (String,
                        Integer,
                        engine_from_config,
                        Column)
from sqlalchemy.ext.declarative import declarative_base
from sqlalchemy.orm import sessionmaker

Base_1 = declarative_base()

Base_2 = declarative_base()

aurthurm

# -*- coding:utf8 -*-
import re

from flask import Flask

from flask_sqlalchemy import SQLAlchemy as BaseSQLAlchemy
from flask_sqlalchemy import _SignallingSession as BaseSignallingSession
from flask_sqlalchemy import orm, partial, get_state

from datetime import datetime

aurthurm

System Design Cheatsheet

Picking the right architecture = Picking the right battles + Managing trade-offs

Basic Steps

1. Clarify and agree on the scope of the system

• User cases (description of sequences of events that, taken together, lead to a system doing something useful)
  • Who is going to use it?
  • How are they going to use it?

aurthurm

'''
Convert Yelp Academic Dataset from JSON to CSV

Requires Pandas (https://pypi.python.org/pypi/pandas)

By Paul Butler, No Rights Reserved
'''

import json
import pandas as pd